3BXO

Crystal Structure of Streptomyces venezuelae DesVI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Three-Dimensional Structure of DesVI from Streptomyces venezuelae: A Sugar N,N-Dimethyltransferase Required for dTDP-Desosamine Biosynthesis.

Burgie, E.S.Holden, H.M.

(2008) Biochemistry 47: 3982-3988

  • DOI: 10.1021/bi800063j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • D-Desosamine, or 3-(dimethylamino)-3,4,6-trideoxyglucose, is an unusual sugar found on the macrolide antibiotic erythromycin, and it has been shown to play a critical role in the biological activity of the drug. Desosamine is added to the parent agly ...

    D-Desosamine, or 3-(dimethylamino)-3,4,6-trideoxyglucose, is an unusual sugar found on the macrolide antibiotic erythromycin, and it has been shown to play a critical role in the biological activity of the drug. Desosamine is added to the parent aglycone via the action of a glycosyltransferase that utilizes dTDP-desosamine as its substrate. Six enzymes are required for the biosynthesis of dTDP-desosamine in Streptomyces venezuelae, with the last step catalyzed by DesVI, an N, N-dimethyltransferase. Here we describe the X-ray crystal structure determined to 2.0 A resolution of DesVI complexed with S-adenosylmethionine (SAM) and the substrate analogue UDP-benzene. Each subunit of the DesVI dimer contains a seven-stranded mixed beta-sheet flanked on either side by alpha-helices. In addition to this major tertiary structural element, there is a four-stranded antiparallel beta-sheet that provides the platform necessary for subunit-subunit assembly. On the basis of the UDP-benzene binding mode, the DesVI substrate, dTDP-3-(methylamino)-3,4,6-trideoxyglucose, has been modeled into the active site. This model places the C-6' methyl group of the sugar into a hydrophobic patch that is well-conserved among putative nucleotide-linked sugar dimethyltransferases. It is formed by Trp 140, Met 178, and Ile 200. The sugar C-2' hydroxyl sits near Tyr 14, and its C-3' amino group is properly positioned for direct in-line attack of the cofactor's reactive methyl group. While methyltransferases that catalyze single alkylations at carbons, oxygens, sulfurs, and nitrogens have been well characterized, little is known regarding enzymes capable of N,N-dimethylation reactions. As such, the ternary structure of DesVI reported here serves as a structural paradigm for a new family of dimethyltransferases that function on nucleotide-linked sugars.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N,N-dimethyltransferaseA, B239Streptomyces venezuelaeMutation(s): 0 
Gene Names: desVI
EC: 2.1.1.234
Find proteins for Q9ZGH6 (Streptomyces venezuelae)
Explore Q9ZGH6 
Go to UniProtKB:  Q9ZGH6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UPP
Query on UPP

Download CCD File 
A, B
PHENYL-URIDINE-5'-DIPHOSPHATE
C15 H18 N2 O12 P2
ZHUWBKDWWGKIEN-FMKGYKFTSA-N
 Ligand Interaction
SAM
Query on SAM

Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.17α = 90
b = 56.096β = 92.5
c = 116.482γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
PHASERphasing
SOLVEphasing
DMphasing
TNTrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance